Please make sure your are using the “…gene_exp.diff” file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has all columns populated. See below for specific columns that must be present.

Yes, there are a few ways that you can experience all of the functionalities of iPathwayGuide. We provide several demo analyses that are automatically shared when you register for a free account. These datasets cover a range of experiment types, conditions, and analysis outcomes. You have full access to interact with all of the demo analyses and experience all of the features of iPathwayGuide. We also provide sample data files, which allows you to try out the data intake process before uploading your own data.

You can analyze a complete experiment for only $149. This will provide a full interactive report that you can use to further explore your results in many ways, including discovering mechanisms. The interactive report can be shared with others at no additional cost. The price also includes a PDF report that many of our users use as the Methods or Supplementary Materials in their published peer-reviewed articles. This automatically-generated PDF contains a full description of your input data, experiment, methods, results with figures, and references.

Yes! From the dashboard, just click share on any completed report. Then enter the email address for the person you wish to share it with. If they do not have an account, they will be prompted to create on. Once registered, they will be able to view the report.

iPathwayGuide works with the most popular differential expression files. Some 3rd party emulators (e.g. Galaxy) may structure their data slightly differently. Click on the sample files below to see the structure of these files.

• “This software analysis tool implements the ‘Impact Analysis’ 1 approach that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc., as described in (Draghici, 2007, Donato, 2013).”

GEO2R does not perform normalization for Affymetrix CEL files. The Advaita iPathwayGuide CEL file uploader currently utilizes the Gene-chip Robust Multi-array Average (GCRMA) normalization method. As such, there can be discrepancies between CEL files processed with GEO2R vs. iPathwayGuide.

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